## Error in library(future.apply) : 
##   there is no package called 'future.apply'

Project info

Samples: dcDNA Seq
pychopper: no
mapping version: v6
LoRTIA: yes (stranded only output)

Normalization: Viral read count

Canonic TSS dynamics

Those reads were counted only, where the 5-prime adapters were “correct” (according to LoRTIA)

Statistics of counts

Difference from mean

Varcoeff

Clustering of samples

## Bootstrap (r = 0.49)... Done.
## Bootstrap (r = 0.59)... Done.
## Bootstrap (r = 0.7)... Done.
## Bootstrap (r = 0.8)... Done.
## Bootstrap (r = 0.9)... Done.
## Bootstrap (r = 1.0)... Done.
## Bootstrap (r = 1.09)... Done.
## Bootstrap (r = 1.19)... Done.
## Bootstrap (r = 1.29)... Done.
## Bootstrap (r = 1.39)... Done.

The sample 48h_3 stands out!

Filtering of samples

Clustering of genes into de-novo clusters using hierarchial clustering

Cluster memberships

## Bootstrap (r = 0.48)... Done.
## Bootstrap (r = 0.59)... Done.
## Bootstrap (r = 0.67)... Done.
## Bootstrap (r = 0.78)... Done.
## Bootstrap (r = 0.89)... Done.
## Bootstrap (r = 1.0)... Done.
## Bootstrap (r = 1.07)... Done.
## Bootstrap (r = 1.19)... Done.
## Bootstrap (r = 1.3)... Done.
## Bootstrap (r = 1.37)... Done.

Optimal number of clusters

Find the optimal number of clusters to cut the tree at and calculate

Clustering statistics: Cluster number: 5

## Key: <cluster>
##     cluster    gene        si        au        bp       se.si        se.au
##       <int>  <char>     <num>     <num>     <num>       <num>        <num>
##  1:       1    ORF1 0.9886267 0.9982085 0.8168145 0.002477789 0.0004963390
##  2:       1    ORF4 0.9886267 0.9982085 0.8168145 0.002477789 0.0004963390
##  3:       1    ORF5 0.9886267 0.9982085 0.8168145 0.002477789 0.0004963390
##  4:       1    ORF7 0.9886267 0.9982085 0.8168145 0.002477789 0.0004963390
##  5:       1    ORF9 0.9886267 0.9982085 0.8168145 0.002477789 0.0004963390
##  6:       1   ORF10 0.9886267 0.9982085 0.8168145 0.002477789 0.0004963390
##  7:       1   ORF17 0.9886267 0.9982085 0.8168145 0.002477789 0.0004963390
##  8:       1   ORF20 0.9886267 0.9982085 0.8168145 0.002477789 0.0004963390
##  9:       1   ORF21 0.9886267 0.9982085 0.8168145 0.002477789 0.0004963390
## 10:       1   ORF30 0.9886267 0.9982085 0.8168145 0.002477789 0.0004963390
## 11:       1   ORF31 0.9886267 0.9982085 0.8168145 0.002477789 0.0004963390
## 12:       1   ORF32 0.9886267 0.9982085 0.8168145 0.002477789 0.0004963390
## 13:       1   ORF34 0.9886267 0.9982085 0.8168145 0.002477789 0.0004963390
## 14:       1   ORF38 0.9886267 0.9982085 0.8168145 0.002477789 0.0004963390
## 15:       1   ORF50 0.9886267 0.9982085 0.8168145 0.002477789 0.0004963390
## 16:       1   ORF53 0.9886267 0.9982085 0.8168145 0.002477789 0.0004963390
## 17:       1   ORF56 0.9886267 0.9982085 0.8168145 0.002477789 0.0004963390
## 18:       1   ORF61 0.9886267 0.9982085 0.8168145 0.002477789 0.0004963390
## 19:       1   ORF63 0.9886267 0.9982085 0.8168145 0.002477789 0.0004963390
## 20:       1  NOIR_1 0.9886267 0.9982085 0.8168145 0.002477789 0.0004963390
## 21:       1 ORF65_1 0.9886267 0.9982085 0.8168145 0.002477789 0.0004963390
## 22:       1 ORF67_1 0.9886267 0.9982085 0.8168145 0.002477789 0.0004963390
## 23:       1   ORF69 0.9886267 0.9982085 0.8168145 0.002477789 0.0004963390
## 24:       1  NOIR_2 0.9886267 0.9982085 0.8168145 0.002477789 0.0004963390
## 25:       2    ORF2 0.7943269 0.9455606 0.6350814 0.023059291 0.0085043753
## 26:       2    ORF3 0.7943269 0.9455606 0.6350814 0.023059291 0.0085043753
## 27:       2   ORF11 0.7943269 0.9455606 0.6350814 0.023059291 0.0085043753
## 28:       2   ORF14 0.7943269 0.9455606 0.6350814 0.023059291 0.0085043753
## 29:       2   ORF18 0.7943269 0.9455606 0.6350814 0.023059291 0.0085043753
## 30:       2   ORF19 0.7943269 0.9455606 0.6350814 0.023059291 0.0085043753
## 31:       2   ORF26 0.7943269 0.9455606 0.6350814 0.023059291 0.0085043753
## 32:       2   ORF28 0.7943269 0.9455606 0.6350814 0.023059291 0.0085043753
## 33:       2   ORF29 0.7943269 0.9455606 0.6350814 0.023059291 0.0085043753
## 34:       2   ORF37 0.7943269 0.9455606 0.6350814 0.023059291 0.0085043753
## 35:       2   ORF49 0.7943269 0.9455606 0.6350814 0.023059291 0.0085043753
## 36:       2   ORF51 0.7943269 0.9455606 0.6350814 0.023059291 0.0085043753
## 37:       2   ORF55 0.7943269 0.9455606 0.6350814 0.023059291 0.0085043753
## 38:       2 ORF66_1 0.7943269 0.9455606 0.6350814 0.023059291 0.0085043753
## 39:       2   ORF73 0.7943269 0.9455606 0.6350814 0.023059291 0.0085043753
## 40:       2   ORF74 0.7943269 0.9455606 0.6350814 0.023059291 0.0085043753
## 41:       2   ORF76 0.7943269 0.9455606 0.6350814 0.023059291 0.0085043753
## 42:       3    ORF6 0.9936064 0.9991577 0.8171322 0.001491305 0.0002494995
## 43:       3   ORF70 0.9936064 0.9991577 0.8171322 0.001491305 0.0002494995
## 44:       4    ORF8 0.9056246 0.9834563 0.6041646 0.013300135 0.0032140854
## 45:       4   ORF12 0.9056246 0.9834563 0.6041646 0.013300135 0.0032140854
## 46:       4   ORF13 0.9056246 0.9834563 0.6041646 0.013300135 0.0032140854
## 47:       4   ORF15 0.9056246 0.9834563 0.6041646 0.013300135 0.0032140854
## 48:       4   ORF16 0.9056246 0.9834563 0.6041646 0.013300135 0.0032140854
## 49:       4   ORF22 0.9056246 0.9834563 0.6041646 0.013300135 0.0032140854
## 50:       4   ORF23 0.9056246 0.9834563 0.6041646 0.013300135 0.0032140854
## 51:       4   ORF24 0.9056246 0.9834563 0.6041646 0.013300135 0.0032140854
## 52:       4   ORF25 0.9056246 0.9834563 0.6041646 0.013300135 0.0032140854
## 53:       4   ORF27 0.9056246 0.9834563 0.6041646 0.013300135 0.0032140854
## 54:       4   ORF33 0.9056246 0.9834563 0.6041646 0.013300135 0.0032140854
## 55:       4 ORF35.5 0.9056246 0.9834563 0.6041646 0.013300135 0.0032140854
## 56:       4   ORF35 0.9056246 0.9834563 0.6041646 0.013300135 0.0032140854
## 57:       4   ORF36 0.9056246 0.9834563 0.6041646 0.013300135 0.0032140854
## 58:       4   ORF39 0.9056246 0.9834563 0.6041646 0.013300135 0.0032140854
## 59:       4     CTO 0.9056246 0.9834563 0.6041646 0.013300135 0.0032140854
## 60:       4   ORF40 0.9056246 0.9834563 0.6041646 0.013300135 0.0032140854
## 61:       4   ORF41 0.9056246 0.9834563 0.6041646 0.013300135 0.0032140854
## 62:       4   ORF42 0.9056246 0.9834563 0.6041646 0.013300135 0.0032140854
## 63:       4   ORF43 0.9056246 0.9834563 0.6041646 0.013300135 0.0032140854
## 64:       4   ORF44 0.9056246 0.9834563 0.6041646 0.013300135 0.0032140854
## 65:       4   ORF45 0.9056246 0.9834563 0.6041646 0.013300135 0.0032140854
## 66:       4   ORF46 0.9056246 0.9834563 0.6041646 0.013300135 0.0032140854
## 67:       4   ORF48 0.9056246 0.9834563 0.6041646 0.013300135 0.0032140854
## 68:       4   ORF52 0.9056246 0.9834563 0.6041646 0.013300135 0.0032140854
## 69:       4   ORF54 0.9056246 0.9834563 0.6041646 0.013300135 0.0032140854
## 70:       4   ORF57 0.9056246 0.9834563 0.6041646 0.013300135 0.0032140854
## 71:       4   ORF58 0.9056246 0.9834563 0.6041646 0.013300135 0.0032140854
## 72:       4   ORF59 0.9056246 0.9834563 0.6041646 0.013300135 0.0032140854
## 73:       4   ORF60 0.9056246 0.9834563 0.6041646 0.013300135 0.0032140854
## 74:       4   ORF62 0.9056246 0.9834563 0.6041646 0.013300135 0.0032140854
## 75:       4   ORF68 0.9056246 0.9834563 0.6041646 0.013300135 0.0032140854
## 76:       4   ORF71 0.9056246 0.9834563 0.6041646 0.013300135 0.0032140854
## 77:       4   ORF72 0.9056246 0.9834563 0.6041646 0.013300135 0.0032140854
## 78:       5 ORF64_1 0.8075925 0.9715685 0.4255348 0.023970405 0.0052270304
## 79:       5   ORF75 0.8075925 0.9715685 0.4255348 0.023970405 0.0052270304
##     cluster    gene        si        au        bp       se.si        se.au
##           se.bp          v         c      pchi
##           <num>      <num>     <num>     <num>
##  1: 0.004382320 -1.9080042 1.0047125 0.7086633
##  2: 0.004382320 -1.9080042 1.0047125 0.7086633
##  3: 0.004382320 -1.9080042 1.0047125 0.7086633
##  4: 0.004382320 -1.9080042 1.0047125 0.7086633
##  5: 0.004382320 -1.9080042 1.0047125 0.7086633
##  6: 0.004382320 -1.9080042 1.0047125 0.7086633
##  7: 0.004382320 -1.9080042 1.0047125 0.7086633
##  8: 0.004382320 -1.9080042 1.0047125 0.7086633
##  9: 0.004382320 -1.9080042 1.0047125 0.7086633
## 10: 0.004382320 -1.9080042 1.0047125 0.7086633
## 11: 0.004382320 -1.9080042 1.0047125 0.7086633
## 12: 0.004382320 -1.9080042 1.0047125 0.7086633
## 13: 0.004382320 -1.9080042 1.0047125 0.7086633
## 14: 0.004382320 -1.9080042 1.0047125 0.7086633
## 15: 0.004382320 -1.9080042 1.0047125 0.7086633
## 16: 0.004382320 -1.9080042 1.0047125 0.7086633
## 17: 0.004382320 -1.9080042 1.0047125 0.7086633
## 18: 0.004382320 -1.9080042 1.0047125 0.7086633
## 19: 0.004382320 -1.9080042 1.0047125 0.7086633
## 20: 0.004382320 -1.9080042 1.0047125 0.7086633
## 21: 0.004382320 -1.9080042 1.0047125 0.7086633
## 22: 0.004382320 -1.9080042 1.0047125 0.7086633
## 23: 0.004382320 -1.9080042 1.0047125 0.7086633
## 24: 0.004382320 -1.9080042 1.0047125 0.7086633
## 25: 0.005151593 -0.9742975 0.6289552 0.1611733
## 26: 0.005151593 -0.9742975 0.6289552 0.1611733
## 27: 0.005151593 -0.9742975 0.6289552 0.1611733
## 28: 0.005151593 -0.9742975 0.6289552 0.1611733
## 29: 0.005151593 -0.9742975 0.6289552 0.1611733
## 30: 0.005151593 -0.9742975 0.6289552 0.1611733
## 31: 0.005151593 -0.9742975 0.6289552 0.1611733
## 32: 0.005151593 -0.9742975 0.6289552 0.1611733
## 33: 0.005151593 -0.9742975 0.6289552 0.1611733
## 34: 0.005151593 -0.9742975 0.6289552 0.1611733
## 35: 0.005151593 -0.9742975 0.6289552 0.1611733
## 36: 0.005151593 -0.9742975 0.6289552 0.1611733
## 37: 0.005151593 -0.9742975 0.6289552 0.1611733
## 38: 0.005151593 -0.9742975 0.6289552 0.1611733
## 39: 0.005151593 -0.9742975 0.6289552 0.1611733
## 40: 0.005151593 -0.9742975 0.6289552 0.1611733
## 41: 0.005151593 -0.9742975 0.6289552 0.1611733
## 42: 0.004380733 -2.0226622 1.1181723 0.2380321
## 43: 0.004380733 -2.0226622 1.1181723 0.2380321
## 44: 0.005264210 -1.1975818 0.9334403 0.7481233
## 45: 0.005264210 -1.1975818 0.9334403 0.7481233
## 46: 0.005264210 -1.1975818 0.9334403 0.7481233
## 47: 0.005264210 -1.1975818 0.9334403 0.7481233
## 48: 0.005264210 -1.1975818 0.9334403 0.7481233
## 49: 0.005264210 -1.1975818 0.9334403 0.7481233
## 50: 0.005264210 -1.1975818 0.9334403 0.7481233
## 51: 0.005264210 -1.1975818 0.9334403 0.7481233
## 52: 0.005264210 -1.1975818 0.9334403 0.7481233
## 53: 0.005264210 -1.1975818 0.9334403 0.7481233
## 54: 0.005264210 -1.1975818 0.9334403 0.7481233
## 55: 0.005264210 -1.1975818 0.9334403 0.7481233
## 56: 0.005264210 -1.1975818 0.9334403 0.7481233
## 57: 0.005264210 -1.1975818 0.9334403 0.7481233
## 58: 0.005264210 -1.1975818 0.9334403 0.7481233
## 59: 0.005264210 -1.1975818 0.9334403 0.7481233
## 60: 0.005264210 -1.1975818 0.9334403 0.7481233
## 61: 0.005264210 -1.1975818 0.9334403 0.7481233
## 62: 0.005264210 -1.1975818 0.9334403 0.7481233
## 63: 0.005264210 -1.1975818 0.9334403 0.7481233
## 64: 0.005264210 -1.1975818 0.9334403 0.7481233
## 65: 0.005264210 -1.1975818 0.9334403 0.7481233
## 66: 0.005264210 -1.1975818 0.9334403 0.7481233
## 67: 0.005264210 -1.1975818 0.9334403 0.7481233
## 68: 0.005264210 -1.1975818 0.9334403 0.7481233
## 69: 0.005264210 -1.1975818 0.9334403 0.7481233
## 70: 0.005264210 -1.1975818 0.9334403 0.7481233
## 71: 0.005264210 -1.1975818 0.9334403 0.7481233
## 72: 0.005264210 -1.1975818 0.9334403 0.7481233
## 73: 0.005264210 -1.1975818 0.9334403 0.7481233
## 74: 0.005264210 -1.1975818 0.9334403 0.7481233
## 75: 0.005264210 -1.1975818 0.9334403 0.7481233
## 76: 0.005264210 -1.1975818 0.9334403 0.7481233
## 77: 0.005264210 -1.1975818 0.9334403 0.7481233
## 78: 0.005246549 -0.8583044 1.0460582 0.8520751
## 79: 0.005246549 -0.8583044 1.0460582 0.8520751
##           se.bp          v         c      pchi

## [1] "ORF32"   "ORF9"    "ORF67_1" "ORF40"   "ORF59"   "ORF36"   "ORF39"  
## [8] "ORF8"
## [1] 8
##  [1] "ORF2"    "ORF3"    "ORF11"   "ORF14"   "ORF18"   "ORF19"   "ORF26"  
##  [8] "ORF28"   "ORF29"   "ORF37"   "ORF49"   "ORF51"   "ORF55"   "ORF66_1"
## [15] "ORF73"   "ORF74"   "ORF76"
## [1] 17

Clustering statistics: Cluster number: 6

## Key: <cluster>
##     cluster    gene        si        au        bp       se.si        se.au
##       <int>  <char>     <num>     <num>     <num>       <num>        <num>
##  1:       1    ORF1 0.9886267 0.9982085 0.8168145 0.002477789 0.0004963390
##  2:       1    ORF4 0.9886267 0.9982085 0.8168145 0.002477789 0.0004963390
##  3:       1    ORF5 0.9886267 0.9982085 0.8168145 0.002477789 0.0004963390
##  4:       1    ORF7 0.9886267 0.9982085 0.8168145 0.002477789 0.0004963390
##  5:       1    ORF9 0.9886267 0.9982085 0.8168145 0.002477789 0.0004963390
##  6:       1   ORF10 0.9886267 0.9982085 0.8168145 0.002477789 0.0004963390
##  7:       1   ORF17 0.9886267 0.9982085 0.8168145 0.002477789 0.0004963390
##  8:       1   ORF20 0.9886267 0.9982085 0.8168145 0.002477789 0.0004963390
##  9:       1   ORF21 0.9886267 0.9982085 0.8168145 0.002477789 0.0004963390
## 10:       1   ORF30 0.9886267 0.9982085 0.8168145 0.002477789 0.0004963390
## 11:       1   ORF31 0.9886267 0.9982085 0.8168145 0.002477789 0.0004963390
## 12:       1   ORF32 0.9886267 0.9982085 0.8168145 0.002477789 0.0004963390
## 13:       1   ORF34 0.9886267 0.9982085 0.8168145 0.002477789 0.0004963390
## 14:       1   ORF38 0.9886267 0.9982085 0.8168145 0.002477789 0.0004963390
## 15:       1   ORF50 0.9886267 0.9982085 0.8168145 0.002477789 0.0004963390
## 16:       1   ORF53 0.9886267 0.9982085 0.8168145 0.002477789 0.0004963390
## 17:       1   ORF56 0.9886267 0.9982085 0.8168145 0.002477789 0.0004963390
## 18:       1   ORF61 0.9886267 0.9982085 0.8168145 0.002477789 0.0004963390
## 19:       1   ORF63 0.9886267 0.9982085 0.8168145 0.002477789 0.0004963390
## 20:       1  NOIR_1 0.9886267 0.9982085 0.8168145 0.002477789 0.0004963390
## 21:       1 ORF65_1 0.9886267 0.9982085 0.8168145 0.002477789 0.0004963390
## 22:       1 ORF67_1 0.9886267 0.9982085 0.8168145 0.002477789 0.0004963390
## 23:       1   ORF69 0.9886267 0.9982085 0.8168145 0.002477789 0.0004963390
## 24:       1  NOIR_2 0.9886267 0.9982085 0.8168145 0.002477789 0.0004963390
## 25:       2    ORF2 0.7943269 0.9455606 0.6350814 0.023059291 0.0085043753
## 26:       2    ORF3 0.7943269 0.9455606 0.6350814 0.023059291 0.0085043753
## 27:       2   ORF11 0.7943269 0.9455606 0.6350814 0.023059291 0.0085043753
## 28:       2   ORF14 0.7943269 0.9455606 0.6350814 0.023059291 0.0085043753
## 29:       2   ORF18 0.7943269 0.9455606 0.6350814 0.023059291 0.0085043753
## 30:       2   ORF19 0.7943269 0.9455606 0.6350814 0.023059291 0.0085043753
## 31:       2   ORF26 0.7943269 0.9455606 0.6350814 0.023059291 0.0085043753
## 32:       2   ORF28 0.7943269 0.9455606 0.6350814 0.023059291 0.0085043753
## 33:       2   ORF29 0.7943269 0.9455606 0.6350814 0.023059291 0.0085043753
## 34:       2   ORF37 0.7943269 0.9455606 0.6350814 0.023059291 0.0085043753
## 35:       2   ORF49 0.7943269 0.9455606 0.6350814 0.023059291 0.0085043753
## 36:       2   ORF51 0.7943269 0.9455606 0.6350814 0.023059291 0.0085043753
## 37:       2   ORF55 0.7943269 0.9455606 0.6350814 0.023059291 0.0085043753
## 38:       2 ORF66_1 0.7943269 0.9455606 0.6350814 0.023059291 0.0085043753
## 39:       2   ORF73 0.7943269 0.9455606 0.6350814 0.023059291 0.0085043753
## 40:       2   ORF74 0.7943269 0.9455606 0.6350814 0.023059291 0.0085043753
## 41:       2   ORF76 0.7943269 0.9455606 0.6350814 0.023059291 0.0085043753
## 42:       3    ORF6 0.9936064 0.9991577 0.8171322 0.001491305 0.0002494995
## 43:       3   ORF70 0.9936064 0.9991577 0.8171322 0.001491305 0.0002494995
## 44:       4    ORF8 0.9056246 0.9834563 0.6041646 0.013300135 0.0032140854
## 45:       4   ORF12 0.9056246 0.9834563 0.6041646 0.013300135 0.0032140854
## 46:       4   ORF13 0.9056246 0.9834563 0.6041646 0.013300135 0.0032140854
## 47:       4   ORF15 0.9056246 0.9834563 0.6041646 0.013300135 0.0032140854
## 48:       4   ORF16 0.9056246 0.9834563 0.6041646 0.013300135 0.0032140854
## 49:       4   ORF22 0.9056246 0.9834563 0.6041646 0.013300135 0.0032140854
## 50:       4   ORF23 0.9056246 0.9834563 0.6041646 0.013300135 0.0032140854
## 51:       4   ORF24 0.9056246 0.9834563 0.6041646 0.013300135 0.0032140854
## 52:       4   ORF25 0.9056246 0.9834563 0.6041646 0.013300135 0.0032140854
## 53:       4   ORF27 0.9056246 0.9834563 0.6041646 0.013300135 0.0032140854
## 54:       4   ORF33 0.9056246 0.9834563 0.6041646 0.013300135 0.0032140854
## 55:       4 ORF35.5 0.9056246 0.9834563 0.6041646 0.013300135 0.0032140854
## 56:       4   ORF35 0.9056246 0.9834563 0.6041646 0.013300135 0.0032140854
## 57:       4   ORF36 0.9056246 0.9834563 0.6041646 0.013300135 0.0032140854
## 58:       4   ORF39 0.9056246 0.9834563 0.6041646 0.013300135 0.0032140854
## 59:       4     CTO 0.9056246 0.9834563 0.6041646 0.013300135 0.0032140854
## 60:       4   ORF40 0.9056246 0.9834563 0.6041646 0.013300135 0.0032140854
## 61:       4   ORF41 0.9056246 0.9834563 0.6041646 0.013300135 0.0032140854
## 62:       4   ORF42 0.9056246 0.9834563 0.6041646 0.013300135 0.0032140854
## 63:       4   ORF43 0.9056246 0.9834563 0.6041646 0.013300135 0.0032140854
## 64:       4   ORF44 0.9056246 0.9834563 0.6041646 0.013300135 0.0032140854
## 65:       4   ORF46 0.9056246 0.9834563 0.6041646 0.013300135 0.0032140854
## 66:       4   ORF48 0.9056246 0.9834563 0.6041646 0.013300135 0.0032140854
## 67:       4   ORF52 0.9056246 0.9834563 0.6041646 0.013300135 0.0032140854
## 68:       4   ORF54 0.9056246 0.9834563 0.6041646 0.013300135 0.0032140854
## 69:       4   ORF57 0.9056246 0.9834563 0.6041646 0.013300135 0.0032140854
## 70:       4   ORF58 0.9056246 0.9834563 0.6041646 0.013300135 0.0032140854
## 71:       4   ORF59 0.9056246 0.9834563 0.6041646 0.013300135 0.0032140854
## 72:       4   ORF60 0.9056246 0.9834563 0.6041646 0.013300135 0.0032140854
## 73:       4   ORF62 0.9056246 0.9834563 0.6041646 0.013300135 0.0032140854
## 74:       4   ORF68 0.9056246 0.9834563 0.6041646 0.013300135 0.0032140854
## 75:       4   ORF71 0.9056246 0.9834563 0.6041646 0.013300135 0.0032140854
## 76:       4   ORF72 0.9056246 0.9834563 0.6041646 0.013300135 0.0032140854
## 77:       5   ORF45 0.8075925 0.9715685 0.4255348 0.023970405 0.0052270304
## 78:       6 ORF64_1 0.4259739 0.9237294 0.2132357 0.059173405 0.0133606677
## 79:       6   ORF75 0.4259739 0.9237294 0.2132357 0.059173405 0.0133606677
##     cluster    gene        si        au        bp       se.si        se.au
##           se.bp          v         c      pchi
##           <num>      <num>     <num>     <num>
##  1: 0.004382320 -1.9080042 1.0047125 0.7086633
##  2: 0.004382320 -1.9080042 1.0047125 0.7086633
##  3: 0.004382320 -1.9080042 1.0047125 0.7086633
##  4: 0.004382320 -1.9080042 1.0047125 0.7086633
##  5: 0.004382320 -1.9080042 1.0047125 0.7086633
##  6: 0.004382320 -1.9080042 1.0047125 0.7086633
##  7: 0.004382320 -1.9080042 1.0047125 0.7086633
##  8: 0.004382320 -1.9080042 1.0047125 0.7086633
##  9: 0.004382320 -1.9080042 1.0047125 0.7086633
## 10: 0.004382320 -1.9080042 1.0047125 0.7086633
## 11: 0.004382320 -1.9080042 1.0047125 0.7086633
## 12: 0.004382320 -1.9080042 1.0047125 0.7086633
## 13: 0.004382320 -1.9080042 1.0047125 0.7086633
## 14: 0.004382320 -1.9080042 1.0047125 0.7086633
## 15: 0.004382320 -1.9080042 1.0047125 0.7086633
## 16: 0.004382320 -1.9080042 1.0047125 0.7086633
## 17: 0.004382320 -1.9080042 1.0047125 0.7086633
## 18: 0.004382320 -1.9080042 1.0047125 0.7086633
## 19: 0.004382320 -1.9080042 1.0047125 0.7086633
## 20: 0.004382320 -1.9080042 1.0047125 0.7086633
## 21: 0.004382320 -1.9080042 1.0047125 0.7086633
## 22: 0.004382320 -1.9080042 1.0047125 0.7086633
## 23: 0.004382320 -1.9080042 1.0047125 0.7086633
## 24: 0.004382320 -1.9080042 1.0047125 0.7086633
## 25: 0.005151593 -0.9742975 0.6289552 0.1611733
## 26: 0.005151593 -0.9742975 0.6289552 0.1611733
## 27: 0.005151593 -0.9742975 0.6289552 0.1611733
## 28: 0.005151593 -0.9742975 0.6289552 0.1611733
## 29: 0.005151593 -0.9742975 0.6289552 0.1611733
## 30: 0.005151593 -0.9742975 0.6289552 0.1611733
## 31: 0.005151593 -0.9742975 0.6289552 0.1611733
## 32: 0.005151593 -0.9742975 0.6289552 0.1611733
## 33: 0.005151593 -0.9742975 0.6289552 0.1611733
## 34: 0.005151593 -0.9742975 0.6289552 0.1611733
## 35: 0.005151593 -0.9742975 0.6289552 0.1611733
## 36: 0.005151593 -0.9742975 0.6289552 0.1611733
## 37: 0.005151593 -0.9742975 0.6289552 0.1611733
## 38: 0.005151593 -0.9742975 0.6289552 0.1611733
## 39: 0.005151593 -0.9742975 0.6289552 0.1611733
## 40: 0.005151593 -0.9742975 0.6289552 0.1611733
## 41: 0.005151593 -0.9742975 0.6289552 0.1611733
## 42: 0.004380733 -2.0226622 1.1181723 0.2380321
## 43: 0.004380733 -2.0226622 1.1181723 0.2380321
## 44: 0.005264210 -1.1975818 0.9334403 0.7481233
## 45: 0.005264210 -1.1975818 0.9334403 0.7481233
## 46: 0.005264210 -1.1975818 0.9334403 0.7481233
## 47: 0.005264210 -1.1975818 0.9334403 0.7481233
## 48: 0.005264210 -1.1975818 0.9334403 0.7481233
## 49: 0.005264210 -1.1975818 0.9334403 0.7481233
## 50: 0.005264210 -1.1975818 0.9334403 0.7481233
## 51: 0.005264210 -1.1975818 0.9334403 0.7481233
## 52: 0.005264210 -1.1975818 0.9334403 0.7481233
## 53: 0.005264210 -1.1975818 0.9334403 0.7481233
## 54: 0.005264210 -1.1975818 0.9334403 0.7481233
## 55: 0.005264210 -1.1975818 0.9334403 0.7481233
## 56: 0.005264210 -1.1975818 0.9334403 0.7481233
## 57: 0.005264210 -1.1975818 0.9334403 0.7481233
## 58: 0.005264210 -1.1975818 0.9334403 0.7481233
## 59: 0.005264210 -1.1975818 0.9334403 0.7481233
## 60: 0.005264210 -1.1975818 0.9334403 0.7481233
## 61: 0.005264210 -1.1975818 0.9334403 0.7481233
## 62: 0.005264210 -1.1975818 0.9334403 0.7481233
## 63: 0.005264210 -1.1975818 0.9334403 0.7481233
## 64: 0.005264210 -1.1975818 0.9334403 0.7481233
## 65: 0.005264210 -1.1975818 0.9334403 0.7481233
## 66: 0.005264210 -1.1975818 0.9334403 0.7481233
## 67: 0.005264210 -1.1975818 0.9334403 0.7481233
## 68: 0.005264210 -1.1975818 0.9334403 0.7481233
## 69: 0.005264210 -1.1975818 0.9334403 0.7481233
## 70: 0.005264210 -1.1975818 0.9334403 0.7481233
## 71: 0.005264210 -1.1975818 0.9334403 0.7481233
## 72: 0.005264210 -1.1975818 0.9334403 0.7481233
## 73: 0.005264210 -1.1975818 0.9334403 0.7481233
## 74: 0.005264210 -1.1975818 0.9334403 0.7481233
## 75: 0.005264210 -1.1975818 0.9334403 0.7481233
## 76: 0.005264210 -1.1975818 0.9334403 0.7481233
## 77: 0.005246549 -0.8583044 1.0460582 0.8520751
## 78: 0.004298087 -0.3176844 1.1129287 0.5410819
## 79: 0.004298087 -0.3176844 1.1129287 0.5410819
##           se.bp          v         c      pchi

## [1] "ORF32"   "ORF9"    "ORF67_1" "ORF59"   "ORF36"   "ORF8"    "ORF39"
## [1] 7
##  [1] "ORF2"    "ORF3"    "ORF11"   "ORF14"   "ORF18"   "ORF19"   "ORF26"  
##  [8] "ORF28"   "ORF29"   "ORF37"   "ORF49"   "ORF51"   "ORF55"   "ORF66_1"
## [15] "ORF73"   "ORF74"   "ORF76"   "ORF64_1" "ORF75"
## [1] 19

Clustering statistics: Cluster number: 7

## Key: <cluster>
##     cluster    gene        si        au        bp       se.si        se.au
##       <int>  <char>     <num>     <num>     <num>       <num>        <num>
##  1:       1    ORF1 0.9886267 0.9982085 0.8168145 0.002477789 0.0004963390
##  2:       1    ORF5 0.9886267 0.9982085 0.8168145 0.002477789 0.0004963390
##  3:       1   ORF10 0.9886267 0.9982085 0.8168145 0.002477789 0.0004963390
##  4:       1   ORF17 0.9886267 0.9982085 0.8168145 0.002477789 0.0004963390
##  5:       1   ORF30 0.9886267 0.9982085 0.8168145 0.002477789 0.0004963390
##  6:       1   ORF32 0.9886267 0.9982085 0.8168145 0.002477789 0.0004963390
##  7:       1   ORF53 0.9886267 0.9982085 0.8168145 0.002477789 0.0004963390
##  8:       1   ORF63 0.9886267 0.9982085 0.8168145 0.002477789 0.0004963390
##  9:       1 ORF65_1 0.9886267 0.9982085 0.8168145 0.002477789 0.0004963390
## 10:       1 ORF67_1 0.9886267 0.9982085 0.8168145 0.002477789 0.0004963390
## 11:       1   ORF69 0.9886267 0.9982085 0.8168145 0.002477789 0.0004963390
## 12:       1  NOIR_2 0.9886267 0.9982085 0.8168145 0.002477789 0.0004963390
## 13:       2    ORF2 0.7943269 0.9455606 0.6350814 0.023059291 0.0085043753
## 14:       2    ORF3 0.7943269 0.9455606 0.6350814 0.023059291 0.0085043753
## 15:       2   ORF11 0.7943269 0.9455606 0.6350814 0.023059291 0.0085043753
## 16:       2   ORF14 0.7943269 0.9455606 0.6350814 0.023059291 0.0085043753
## 17:       2   ORF18 0.7943269 0.9455606 0.6350814 0.023059291 0.0085043753
## 18:       2   ORF19 0.7943269 0.9455606 0.6350814 0.023059291 0.0085043753
## 19:       2   ORF26 0.7943269 0.9455606 0.6350814 0.023059291 0.0085043753
## 20:       2   ORF28 0.7943269 0.9455606 0.6350814 0.023059291 0.0085043753
## 21:       2   ORF29 0.7943269 0.9455606 0.6350814 0.023059291 0.0085043753
## 22:       2   ORF37 0.7943269 0.9455606 0.6350814 0.023059291 0.0085043753
## 23:       2   ORF49 0.7943269 0.9455606 0.6350814 0.023059291 0.0085043753
## 24:       2   ORF51 0.7943269 0.9455606 0.6350814 0.023059291 0.0085043753
## 25:       2   ORF55 0.7943269 0.9455606 0.6350814 0.023059291 0.0085043753
## 26:       2 ORF66_1 0.7943269 0.9455606 0.6350814 0.023059291 0.0085043753
## 27:       2   ORF73 0.7943269 0.9455606 0.6350814 0.023059291 0.0085043753
## 28:       2   ORF74 0.7943269 0.9455606 0.6350814 0.023059291 0.0085043753
## 29:       2   ORF76 0.7943269 0.9455606 0.6350814 0.023059291 0.0085043753
## 30:       3    ORF4 0.9936064 0.9991577 0.8171322 0.001491305 0.0002494995
## 31:       3    ORF7 0.9936064 0.9991577 0.8171322 0.001491305 0.0002494995
## 32:       3    ORF9 0.9936064 0.9991577 0.8171322 0.001491305 0.0002494995
## 33:       3   ORF20 0.9936064 0.9991577 0.8171322 0.001491305 0.0002494995
## 34:       3   ORF21 0.9936064 0.9991577 0.8171322 0.001491305 0.0002494995
## 35:       3   ORF31 0.9936064 0.9991577 0.8171322 0.001491305 0.0002494995
## 36:       3   ORF34 0.9936064 0.9991577 0.8171322 0.001491305 0.0002494995
## 37:       3   ORF38 0.9936064 0.9991577 0.8171322 0.001491305 0.0002494995
## 38:       3   ORF50 0.9936064 0.9991577 0.8171322 0.001491305 0.0002494995
## 39:       3   ORF56 0.9936064 0.9991577 0.8171322 0.001491305 0.0002494995
## 40:       3   ORF61 0.9936064 0.9991577 0.8171322 0.001491305 0.0002494995
## 41:       3  NOIR_1 0.9936064 0.9991577 0.8171322 0.001491305 0.0002494995
## 42:       4    ORF6 0.9056246 0.9834563 0.6041646 0.013300135 0.0032140854
## 43:       4   ORF70 0.9056246 0.9834563 0.6041646 0.013300135 0.0032140854
## 44:       5    ORF8 0.8075925 0.9715685 0.4255348 0.023970405 0.0052270304
## 45:       5   ORF12 0.8075925 0.9715685 0.4255348 0.023970405 0.0052270304
## 46:       5   ORF13 0.8075925 0.9715685 0.4255348 0.023970405 0.0052270304
## 47:       5   ORF15 0.8075925 0.9715685 0.4255348 0.023970405 0.0052270304
## 48:       5   ORF16 0.8075925 0.9715685 0.4255348 0.023970405 0.0052270304
## 49:       5   ORF22 0.8075925 0.9715685 0.4255348 0.023970405 0.0052270304
## 50:       5   ORF23 0.8075925 0.9715685 0.4255348 0.023970405 0.0052270304
## 51:       5   ORF24 0.8075925 0.9715685 0.4255348 0.023970405 0.0052270304
## 52:       5   ORF25 0.8075925 0.9715685 0.4255348 0.023970405 0.0052270304
## 53:       5   ORF27 0.8075925 0.9715685 0.4255348 0.023970405 0.0052270304
## 54:       5   ORF33 0.8075925 0.9715685 0.4255348 0.023970405 0.0052270304
## 55:       5 ORF35.5 0.8075925 0.9715685 0.4255348 0.023970405 0.0052270304
## 56:       5   ORF35 0.8075925 0.9715685 0.4255348 0.023970405 0.0052270304
## 57:       5   ORF36 0.8075925 0.9715685 0.4255348 0.023970405 0.0052270304
## 58:       5   ORF39 0.8075925 0.9715685 0.4255348 0.023970405 0.0052270304
## 59:       5     CTO 0.8075925 0.9715685 0.4255348 0.023970405 0.0052270304
## 60:       5   ORF40 0.8075925 0.9715685 0.4255348 0.023970405 0.0052270304
## 61:       5   ORF41 0.8075925 0.9715685 0.4255348 0.023970405 0.0052270304
## 62:       5   ORF42 0.8075925 0.9715685 0.4255348 0.023970405 0.0052270304
## 63:       5   ORF43 0.8075925 0.9715685 0.4255348 0.023970405 0.0052270304
## 64:       5   ORF44 0.8075925 0.9715685 0.4255348 0.023970405 0.0052270304
## 65:       5   ORF46 0.8075925 0.9715685 0.4255348 0.023970405 0.0052270304
## 66:       5   ORF48 0.8075925 0.9715685 0.4255348 0.023970405 0.0052270304
## 67:       5   ORF52 0.8075925 0.9715685 0.4255348 0.023970405 0.0052270304
## 68:       5   ORF54 0.8075925 0.9715685 0.4255348 0.023970405 0.0052270304
## 69:       5   ORF57 0.8075925 0.9715685 0.4255348 0.023970405 0.0052270304
## 70:       5   ORF58 0.8075925 0.9715685 0.4255348 0.023970405 0.0052270304
## 71:       5   ORF59 0.8075925 0.9715685 0.4255348 0.023970405 0.0052270304
## 72:       5   ORF60 0.8075925 0.9715685 0.4255348 0.023970405 0.0052270304
## 73:       5   ORF62 0.8075925 0.9715685 0.4255348 0.023970405 0.0052270304
## 74:       5   ORF68 0.8075925 0.9715685 0.4255348 0.023970405 0.0052270304
## 75:       5   ORF71 0.8075925 0.9715685 0.4255348 0.023970405 0.0052270304
## 76:       5   ORF72 0.8075925 0.9715685 0.4255348 0.023970405 0.0052270304
## 77:       6   ORF45 0.4259739 0.9237294 0.2132357 0.059173405 0.0133606677
## 78:       7 ORF64_1 0.7534348 0.9633886 0.3842029 0.029206391 0.0065440020
## 79:       7   ORF75 0.7534348 0.9633886 0.3842029 0.029206391 0.0065440020
##     cluster    gene        si        au        bp       se.si        se.au
##           se.bp          v         c      pchi
##           <num>      <num>     <num>     <num>
##  1: 0.004382320 -1.9080042 1.0047125 0.7086633
##  2: 0.004382320 -1.9080042 1.0047125 0.7086633
##  3: 0.004382320 -1.9080042 1.0047125 0.7086633
##  4: 0.004382320 -1.9080042 1.0047125 0.7086633
##  5: 0.004382320 -1.9080042 1.0047125 0.7086633
##  6: 0.004382320 -1.9080042 1.0047125 0.7086633
##  7: 0.004382320 -1.9080042 1.0047125 0.7086633
##  8: 0.004382320 -1.9080042 1.0047125 0.7086633
##  9: 0.004382320 -1.9080042 1.0047125 0.7086633
## 10: 0.004382320 -1.9080042 1.0047125 0.7086633
## 11: 0.004382320 -1.9080042 1.0047125 0.7086633
## 12: 0.004382320 -1.9080042 1.0047125 0.7086633
## 13: 0.005151593 -0.9742975 0.6289552 0.1611733
## 14: 0.005151593 -0.9742975 0.6289552 0.1611733
## 15: 0.005151593 -0.9742975 0.6289552 0.1611733
## 16: 0.005151593 -0.9742975 0.6289552 0.1611733
## 17: 0.005151593 -0.9742975 0.6289552 0.1611733
## 18: 0.005151593 -0.9742975 0.6289552 0.1611733
## 19: 0.005151593 -0.9742975 0.6289552 0.1611733
## 20: 0.005151593 -0.9742975 0.6289552 0.1611733
## 21: 0.005151593 -0.9742975 0.6289552 0.1611733
## 22: 0.005151593 -0.9742975 0.6289552 0.1611733
## 23: 0.005151593 -0.9742975 0.6289552 0.1611733
## 24: 0.005151593 -0.9742975 0.6289552 0.1611733
## 25: 0.005151593 -0.9742975 0.6289552 0.1611733
## 26: 0.005151593 -0.9742975 0.6289552 0.1611733
## 27: 0.005151593 -0.9742975 0.6289552 0.1611733
## 28: 0.005151593 -0.9742975 0.6289552 0.1611733
## 29: 0.005151593 -0.9742975 0.6289552 0.1611733
## 30: 0.004380733 -2.0226622 1.1181723 0.2380321
## 31: 0.004380733 -2.0226622 1.1181723 0.2380321
## 32: 0.004380733 -2.0226622 1.1181723 0.2380321
## 33: 0.004380733 -2.0226622 1.1181723 0.2380321
## 34: 0.004380733 -2.0226622 1.1181723 0.2380321
## 35: 0.004380733 -2.0226622 1.1181723 0.2380321
## 36: 0.004380733 -2.0226622 1.1181723 0.2380321
## 37: 0.004380733 -2.0226622 1.1181723 0.2380321
## 38: 0.004380733 -2.0226622 1.1181723 0.2380321
## 39: 0.004380733 -2.0226622 1.1181723 0.2380321
## 40: 0.004380733 -2.0226622 1.1181723 0.2380321
## 41: 0.004380733 -2.0226622 1.1181723 0.2380321
## 42: 0.005264210 -1.1975818 0.9334403 0.7481233
## 43: 0.005264210 -1.1975818 0.9334403 0.7481233
## 44: 0.005246549 -0.8583044 1.0460582 0.8520751
## 45: 0.005246549 -0.8583044 1.0460582 0.8520751
## 46: 0.005246549 -0.8583044 1.0460582 0.8520751
## 47: 0.005246549 -0.8583044 1.0460582 0.8520751
## 48: 0.005246549 -0.8583044 1.0460582 0.8520751
## 49: 0.005246549 -0.8583044 1.0460582 0.8520751
## 50: 0.005246549 -0.8583044 1.0460582 0.8520751
## 51: 0.005246549 -0.8583044 1.0460582 0.8520751
## 52: 0.005246549 -0.8583044 1.0460582 0.8520751
## 53: 0.005246549 -0.8583044 1.0460582 0.8520751
## 54: 0.005246549 -0.8583044 1.0460582 0.8520751
## 55: 0.005246549 -0.8583044 1.0460582 0.8520751
## 56: 0.005246549 -0.8583044 1.0460582 0.8520751
## 57: 0.005246549 -0.8583044 1.0460582 0.8520751
## 58: 0.005246549 -0.8583044 1.0460582 0.8520751
## 59: 0.005246549 -0.8583044 1.0460582 0.8520751
## 60: 0.005246549 -0.8583044 1.0460582 0.8520751
## 61: 0.005246549 -0.8583044 1.0460582 0.8520751
## 62: 0.005246549 -0.8583044 1.0460582 0.8520751
## 63: 0.005246549 -0.8583044 1.0460582 0.8520751
## 64: 0.005246549 -0.8583044 1.0460582 0.8520751
## 65: 0.005246549 -0.8583044 1.0460582 0.8520751
## 66: 0.005246549 -0.8583044 1.0460582 0.8520751
## 67: 0.005246549 -0.8583044 1.0460582 0.8520751
## 68: 0.005246549 -0.8583044 1.0460582 0.8520751
## 69: 0.005246549 -0.8583044 1.0460582 0.8520751
## 70: 0.005246549 -0.8583044 1.0460582 0.8520751
## 71: 0.005246549 -0.8583044 1.0460582 0.8520751
## 72: 0.005246549 -0.8583044 1.0460582 0.8520751
## 73: 0.005246549 -0.8583044 1.0460582 0.8520751
## 74: 0.005246549 -0.8583044 1.0460582 0.8520751
## 75: 0.005246549 -0.8583044 1.0460582 0.8520751
## 76: 0.005246549 -0.8583044 1.0460582 0.8520751
## 77: 0.004298087 -0.3176844 1.1129287 0.5410819
## 78: 0.005146050 -0.7484892 1.0429501 0.8028759
## 79: 0.005146050 -0.7484892 1.0429501 0.8028759
##           se.bp          v         c      pchi

## [1] "ORF32" "ORF59" "ORF36" "ORF8"  "ORF39"
## [1] 5
##  [1] "ORF2"    "ORF3"    "ORF11"   "ORF14"   "ORF18"   "ORF19"   "ORF26"  
##  [8] "ORF28"   "ORF29"   "ORF37"   "ORF49"   "ORF51"   "ORF55"   "ORF66_1"
## [15] "ORF73"   "ORF74"   "ORF76"   "ORF45"
## [1] 18

Clustering statistics: Cluster number: 10

## Key: <cluster>
##     cluster    gene        si        au        bp       se.si        se.au
##       <int>  <char>     <num>     <num>     <num>       <num>        <num>
##  1:       1    ORF1 0.9886267 0.9982085 0.8168145 0.002477789 0.0004963390
##  2:       1    ORF5 0.9886267 0.9982085 0.8168145 0.002477789 0.0004963390
##  3:       1   ORF10 0.9886267 0.9982085 0.8168145 0.002477789 0.0004963390
##  4:       1   ORF17 0.9886267 0.9982085 0.8168145 0.002477789 0.0004963390
##  5:       1   ORF30 0.9886267 0.9982085 0.8168145 0.002477789 0.0004963390
##  6:       1   ORF53 0.9886267 0.9982085 0.8168145 0.002477789 0.0004963390
##  7:       1   ORF63 0.9886267 0.9982085 0.8168145 0.002477789 0.0004963390
##  8:       1 ORF65_1 0.9886267 0.9982085 0.8168145 0.002477789 0.0004963390
##  9:       1 ORF67_1 0.9886267 0.9982085 0.8168145 0.002477789 0.0004963390
## 10:       1   ORF69 0.9886267 0.9982085 0.8168145 0.002477789 0.0004963390
## 11:       1  NOIR_2 0.9886267 0.9982085 0.8168145 0.002477789 0.0004963390
## 12:       2    ORF2 0.7943269 0.9455606 0.6350814 0.023059291 0.0085043753
## 13:       2    ORF3 0.7943269 0.9455606 0.6350814 0.023059291 0.0085043753
## 14:       2   ORF11 0.7943269 0.9455606 0.6350814 0.023059291 0.0085043753
## 15:       2   ORF14 0.7943269 0.9455606 0.6350814 0.023059291 0.0085043753
## 16:       2   ORF18 0.7943269 0.9455606 0.6350814 0.023059291 0.0085043753
## 17:       2   ORF19 0.7943269 0.9455606 0.6350814 0.023059291 0.0085043753
## 18:       2   ORF26 0.7943269 0.9455606 0.6350814 0.023059291 0.0085043753
## 19:       2   ORF29 0.7943269 0.9455606 0.6350814 0.023059291 0.0085043753
## 20:       2   ORF37 0.7943269 0.9455606 0.6350814 0.023059291 0.0085043753
## 21:       2   ORF49 0.7943269 0.9455606 0.6350814 0.023059291 0.0085043753
## 22:       2   ORF51 0.7943269 0.9455606 0.6350814 0.023059291 0.0085043753
## 23:       2   ORF55 0.7943269 0.9455606 0.6350814 0.023059291 0.0085043753
## 24:       2 ORF66_1 0.7943269 0.9455606 0.6350814 0.023059291 0.0085043753
## 25:       2   ORF73 0.7943269 0.9455606 0.6350814 0.023059291 0.0085043753
## 26:       2   ORF74 0.7943269 0.9455606 0.6350814 0.023059291 0.0085043753
## 27:       2   ORF76 0.7943269 0.9455606 0.6350814 0.023059291 0.0085043753
## 28:       3    ORF4 0.9936064 0.9991577 0.8171322 0.001491305 0.0002494995
## 29:       3    ORF7 0.9936064 0.9991577 0.8171322 0.001491305 0.0002494995
## 30:       3    ORF9 0.9936064 0.9991577 0.8171322 0.001491305 0.0002494995
## 31:       3   ORF20 0.9936064 0.9991577 0.8171322 0.001491305 0.0002494995
## 32:       3   ORF21 0.9936064 0.9991577 0.8171322 0.001491305 0.0002494995
## 33:       3   ORF31 0.9936064 0.9991577 0.8171322 0.001491305 0.0002494995
## 34:       3   ORF34 0.9936064 0.9991577 0.8171322 0.001491305 0.0002494995
## 35:       3   ORF38 0.9936064 0.9991577 0.8171322 0.001491305 0.0002494995
## 36:       3   ORF50 0.9936064 0.9991577 0.8171322 0.001491305 0.0002494995
## 37:       3   ORF56 0.9936064 0.9991577 0.8171322 0.001491305 0.0002494995
## 38:       3   ORF61 0.9936064 0.9991577 0.8171322 0.001491305 0.0002494995
## 39:       3  NOIR_1 0.9936064 0.9991577 0.8171322 0.001491305 0.0002494995
## 40:       4    ORF6 0.9056246 0.9834563 0.6041646 0.013300135 0.0032140854
## 41:       4   ORF70 0.9056246 0.9834563 0.6041646 0.013300135 0.0032140854
## 42:       5    ORF8 0.8075925 0.9715685 0.4255348 0.023970405 0.0052270304
## 43:       5   ORF22 0.8075925 0.9715685 0.4255348 0.023970405 0.0052270304
## 44:       5   ORF23 0.8075925 0.9715685 0.4255348 0.023970405 0.0052270304
## 45:       5   ORF24 0.8075925 0.9715685 0.4255348 0.023970405 0.0052270304
## 46:       5   ORF25 0.8075925 0.9715685 0.4255348 0.023970405 0.0052270304
## 47:       5   ORF27 0.8075925 0.9715685 0.4255348 0.023970405 0.0052270304
## 48:       5   ORF33 0.8075925 0.9715685 0.4255348 0.023970405 0.0052270304
## 49:       5 ORF35.5 0.8075925 0.9715685 0.4255348 0.023970405 0.0052270304
## 50:       5   ORF36 0.8075925 0.9715685 0.4255348 0.023970405 0.0052270304
## 51:       5   ORF39 0.8075925 0.9715685 0.4255348 0.023970405 0.0052270304
## 52:       5     CTO 0.8075925 0.9715685 0.4255348 0.023970405 0.0052270304
## 53:       5   ORF40 0.8075925 0.9715685 0.4255348 0.023970405 0.0052270304
## 54:       5   ORF42 0.8075925 0.9715685 0.4255348 0.023970405 0.0052270304
## 55:       5   ORF43 0.8075925 0.9715685 0.4255348 0.023970405 0.0052270304
## 56:       5   ORF44 0.8075925 0.9715685 0.4255348 0.023970405 0.0052270304
## 57:       5   ORF46 0.8075925 0.9715685 0.4255348 0.023970405 0.0052270304
## 58:       5   ORF48 0.8075925 0.9715685 0.4255348 0.023970405 0.0052270304
## 59:       5   ORF58 0.8075925 0.9715685 0.4255348 0.023970405 0.0052270304
## 60:       5   ORF59 0.8075925 0.9715685 0.4255348 0.023970405 0.0052270304
## 61:       5   ORF62 0.8075925 0.9715685 0.4255348 0.023970405 0.0052270304
## 62:       5   ORF68 0.8075925 0.9715685 0.4255348 0.023970405 0.0052270304
## 63:       6   ORF12 0.4259739 0.9237294 0.2132357 0.059173405 0.0133606677
## 64:       6   ORF13 0.4259739 0.9237294 0.2132357 0.059173405 0.0133606677
## 65:       6   ORF15 0.4259739 0.9237294 0.2132357 0.059173405 0.0133606677
## 66:       6   ORF16 0.4259739 0.9237294 0.2132357 0.059173405 0.0133606677
## 67:       6   ORF35 0.4259739 0.9237294 0.2132357 0.059173405 0.0133606677
## 68:       6   ORF41 0.4259739 0.9237294 0.2132357 0.059173405 0.0133606677
## 69:       6   ORF52 0.4259739 0.9237294 0.2132357 0.059173405 0.0133606677
## 70:       6   ORF54 0.4259739 0.9237294 0.2132357 0.059173405 0.0133606677
## 71:       6   ORF57 0.4259739 0.9237294 0.2132357 0.059173405 0.0133606677
## 72:       6   ORF60 0.4259739 0.9237294 0.2132357 0.059173405 0.0133606677
## 73:       6   ORF71 0.4259739 0.9237294 0.2132357 0.059173405 0.0133606677
## 74:       6   ORF72 0.4259739 0.9237294 0.2132357 0.059173405 0.0133606677
## 75:       7   ORF28 0.7534348 0.9633886 0.3842029 0.029206391 0.0065440020
## 76:       8   ORF32 0.6952835 0.9537163 0.3539399 0.034395509 0.0080458063
## 77:       9   ORF45 0.8227913 0.9727877 0.4525900 0.022285232 0.0049976989
## 78:      10 ORF64_1 0.7397556 0.9733276 0.2732995 0.034743538 0.0055867404
## 79:      10   ORF75 0.7397556 0.9733276 0.2732995 0.034743538 0.0055867404
##     cluster    gene        si        au        bp       se.si        se.au
##           se.bp          v         c      pchi
##           <num>      <num>     <num>     <num>
##  1: 0.004382320 -1.9080042 1.0047125 0.7086633
##  2: 0.004382320 -1.9080042 1.0047125 0.7086633
##  3: 0.004382320 -1.9080042 1.0047125 0.7086633
##  4: 0.004382320 -1.9080042 1.0047125 0.7086633
##  5: 0.004382320 -1.9080042 1.0047125 0.7086633
##  6: 0.004382320 -1.9080042 1.0047125 0.7086633
##  7: 0.004382320 -1.9080042 1.0047125 0.7086633
##  8: 0.004382320 -1.9080042 1.0047125 0.7086633
##  9: 0.004382320 -1.9080042 1.0047125 0.7086633
## 10: 0.004382320 -1.9080042 1.0047125 0.7086633
## 11: 0.004382320 -1.9080042 1.0047125 0.7086633
## 12: 0.005151593 -0.9742975 0.6289552 0.1611733
## 13: 0.005151593 -0.9742975 0.6289552 0.1611733
## 14: 0.005151593 -0.9742975 0.6289552 0.1611733
## 15: 0.005151593 -0.9742975 0.6289552 0.1611733
## 16: 0.005151593 -0.9742975 0.6289552 0.1611733
## 17: 0.005151593 -0.9742975 0.6289552 0.1611733
## 18: 0.005151593 -0.9742975 0.6289552 0.1611733
## 19: 0.005151593 -0.9742975 0.6289552 0.1611733
## 20: 0.005151593 -0.9742975 0.6289552 0.1611733
## 21: 0.005151593 -0.9742975 0.6289552 0.1611733
## 22: 0.005151593 -0.9742975 0.6289552 0.1611733
## 23: 0.005151593 -0.9742975 0.6289552 0.1611733
## 24: 0.005151593 -0.9742975 0.6289552 0.1611733
## 25: 0.005151593 -0.9742975 0.6289552 0.1611733
## 26: 0.005151593 -0.9742975 0.6289552 0.1611733
## 27: 0.005151593 -0.9742975 0.6289552 0.1611733
## 28: 0.004380733 -2.0226622 1.1181723 0.2380321
## 29: 0.004380733 -2.0226622 1.1181723 0.2380321
## 30: 0.004380733 -2.0226622 1.1181723 0.2380321
## 31: 0.004380733 -2.0226622 1.1181723 0.2380321
## 32: 0.004380733 -2.0226622 1.1181723 0.2380321
## 33: 0.004380733 -2.0226622 1.1181723 0.2380321
## 34: 0.004380733 -2.0226622 1.1181723 0.2380321
## 35: 0.004380733 -2.0226622 1.1181723 0.2380321
## 36: 0.004380733 -2.0226622 1.1181723 0.2380321
## 37: 0.004380733 -2.0226622 1.1181723 0.2380321
## 38: 0.004380733 -2.0226622 1.1181723 0.2380321
## 39: 0.004380733 -2.0226622 1.1181723 0.2380321
## 40: 0.005264210 -1.1975818 0.9334403 0.7481233
## 41: 0.005264210 -1.1975818 0.9334403 0.7481233
## 42: 0.005246549 -0.8583044 1.0460582 0.8520751
## 43: 0.005246549 -0.8583044 1.0460582 0.8520751
## 44: 0.005246549 -0.8583044 1.0460582 0.8520751
## 45: 0.005246549 -0.8583044 1.0460582 0.8520751
## 46: 0.005246549 -0.8583044 1.0460582 0.8520751
## 47: 0.005246549 -0.8583044 1.0460582 0.8520751
## 48: 0.005246549 -0.8583044 1.0460582 0.8520751
## 49: 0.005246549 -0.8583044 1.0460582 0.8520751
## 50: 0.005246549 -0.8583044 1.0460582 0.8520751
## 51: 0.005246549 -0.8583044 1.0460582 0.8520751
## 52: 0.005246549 -0.8583044 1.0460582 0.8520751
## 53: 0.005246549 -0.8583044 1.0460582 0.8520751
## 54: 0.005246549 -0.8583044 1.0460582 0.8520751
## 55: 0.005246549 -0.8583044 1.0460582 0.8520751
## 56: 0.005246549 -0.8583044 1.0460582 0.8520751
## 57: 0.005246549 -0.8583044 1.0460582 0.8520751
## 58: 0.005246549 -0.8583044 1.0460582 0.8520751
## 59: 0.005246549 -0.8583044 1.0460582 0.8520751
## 60: 0.005246549 -0.8583044 1.0460582 0.8520751
## 61: 0.005246549 -0.8583044 1.0460582 0.8520751
## 62: 0.005246549 -0.8583044 1.0460582 0.8520751
## 63: 0.004298087 -0.3176844 1.1129287 0.5410819
## 64: 0.004298087 -0.3176844 1.1129287 0.5410819
## 65: 0.004298087 -0.3176844 1.1129287 0.5410819
## 66: 0.004298087 -0.3176844 1.1129287 0.5410819
## 67: 0.004298087 -0.3176844 1.1129287 0.5410819
## 68: 0.004298087 -0.3176844 1.1129287 0.5410819
## 69: 0.004298087 -0.3176844 1.1129287 0.5410819
## 70: 0.004298087 -0.3176844 1.1129287 0.5410819
## 71: 0.004298087 -0.3176844 1.1129287 0.5410819
## 72: 0.004298087 -0.3176844 1.1129287 0.5410819
## 73: 0.004298087 -0.3176844 1.1129287 0.5410819
## 74: 0.004298087 -0.3176844 1.1129287 0.5410819
## 75: 0.005146050 -0.7484892 1.0429501 0.8028759
## 76: 0.005047109 -0.6536509 1.0283561 0.0472282
## 77: 0.005288818 -0.9021608 1.0212811 0.7119572
## 78: 0.004694626 -0.6646276 1.2674918 0.5687337
## 79: 0.004694626 -0.6646276 1.2674918 0.5687337
##           se.bp          v         c      pchi

## [1] "ORF49" "ORF74" "ORF55" "ORF73" "ORF62" "ORF48"
## [1] 6
##  [1] "ORF2"    "ORF3"    "ORF11"   "ORF14"   "ORF18"   "ORF19"   "ORF26"  
##  [8] "ORF29"   "ORF37"   "ORF49"   "ORF51"   "ORF55"   "ORF66_1" "ORF73"  
## [15] "ORF74"   "ORF76"   "ORF12"   "ORF13"   "ORF15"   "ORF16"   "ORF35"  
## [22] "ORF41"   "ORF52"   "ORF54"   "ORF57"   "ORF60"   "ORF71"   "ORF72"
## [1] 28

Clustering statistics: Cluster number: 12

## Key: <cluster>
##     cluster    gene        si        au        bp       se.si        se.au
##       <int>  <char>     <num>     <num>     <num>       <num>        <num>
##  1:       1    ORF1 0.9886267 0.9982085 0.8168145 0.002477789 0.0004963390
##  2:       1    ORF5 0.9886267 0.9982085 0.8168145 0.002477789 0.0004963390
##  3:       1   ORF10 0.9886267 0.9982085 0.8168145 0.002477789 0.0004963390
##  4:       1   ORF17 0.9886267 0.9982085 0.8168145 0.002477789 0.0004963390
##  5:       1   ORF30 0.9886267 0.9982085 0.8168145 0.002477789 0.0004963390
##  6:       1   ORF53 0.9886267 0.9982085 0.8168145 0.002477789 0.0004963390
##  7:       1   ORF63 0.9886267 0.9982085 0.8168145 0.002477789 0.0004963390
##  8:       1 ORF65_1 0.9886267 0.9982085 0.8168145 0.002477789 0.0004963390
##  9:       1 ORF67_1 0.9886267 0.9982085 0.8168145 0.002477789 0.0004963390
## 10:       1   ORF69 0.9886267 0.9982085 0.8168145 0.002477789 0.0004963390
## 11:       1  NOIR_2 0.9886267 0.9982085 0.8168145 0.002477789 0.0004963390
## 12:       2    ORF2 0.7943269 0.9455606 0.6350814 0.023059291 0.0085043753
## 13:       2    ORF3 0.7943269 0.9455606 0.6350814 0.023059291 0.0085043753
## 14:       2   ORF11 0.7943269 0.9455606 0.6350814 0.023059291 0.0085043753
## 15:       2   ORF14 0.7943269 0.9455606 0.6350814 0.023059291 0.0085043753
## 16:       2   ORF18 0.7943269 0.9455606 0.6350814 0.023059291 0.0085043753
## 17:       2   ORF19 0.7943269 0.9455606 0.6350814 0.023059291 0.0085043753
## 18:       2   ORF26 0.7943269 0.9455606 0.6350814 0.023059291 0.0085043753
## 19:       2   ORF29 0.7943269 0.9455606 0.6350814 0.023059291 0.0085043753
## 20:       2   ORF49 0.7943269 0.9455606 0.6350814 0.023059291 0.0085043753
## 21:       2 ORF66_1 0.7943269 0.9455606 0.6350814 0.023059291 0.0085043753
## 22:       2   ORF73 0.7943269 0.9455606 0.6350814 0.023059291 0.0085043753
## 23:       2   ORF74 0.7943269 0.9455606 0.6350814 0.023059291 0.0085043753
## 24:       3    ORF4 0.9936064 0.9991577 0.8171322 0.001491305 0.0002494995
## 25:       3    ORF9 0.9936064 0.9991577 0.8171322 0.001491305 0.0002494995
## 26:       3   ORF20 0.9936064 0.9991577 0.8171322 0.001491305 0.0002494995
## 27:       3   ORF21 0.9936064 0.9991577 0.8171322 0.001491305 0.0002494995
## 28:       3   ORF31 0.9936064 0.9991577 0.8171322 0.001491305 0.0002494995
## 29:       3   ORF34 0.9936064 0.9991577 0.8171322 0.001491305 0.0002494995
## 30:       3   ORF38 0.9936064 0.9991577 0.8171322 0.001491305 0.0002494995
## 31:       3   ORF50 0.9936064 0.9991577 0.8171322 0.001491305 0.0002494995
## 32:       3   ORF61 0.9936064 0.9991577 0.8171322 0.001491305 0.0002494995
## 33:       4    ORF6 0.9056246 0.9834563 0.6041646 0.013300135 0.0032140854
## 34:       4   ORF70 0.9056246 0.9834563 0.6041646 0.013300135 0.0032140854
## 35:       5    ORF7 0.8075925 0.9715685 0.4255348 0.023970405 0.0052270304
## 36:       5   ORF56 0.8075925 0.9715685 0.4255348 0.023970405 0.0052270304
## 37:       5  NOIR_1 0.8075925 0.9715685 0.4255348 0.023970405 0.0052270304
## 38:       6    ORF8 0.4259739 0.9237294 0.2132357 0.059173405 0.0133606677
## 39:       6   ORF22 0.4259739 0.9237294 0.2132357 0.059173405 0.0133606677
## 40:       6   ORF23 0.4259739 0.9237294 0.2132357 0.059173405 0.0133606677
## 41:       6   ORF24 0.4259739 0.9237294 0.2132357 0.059173405 0.0133606677
## 42:       6   ORF25 0.4259739 0.9237294 0.2132357 0.059173405 0.0133606677
## 43:       6   ORF27 0.4259739 0.9237294 0.2132357 0.059173405 0.0133606677
## 44:       6   ORF33 0.4259739 0.9237294 0.2132357 0.059173405 0.0133606677
## 45:       6 ORF35.5 0.4259739 0.9237294 0.2132357 0.059173405 0.0133606677
## 46:       6   ORF36 0.4259739 0.9237294 0.2132357 0.059173405 0.0133606677
## 47:       6   ORF39 0.4259739 0.9237294 0.2132357 0.059173405 0.0133606677
## 48:       6     CTO 0.4259739 0.9237294 0.2132357 0.059173405 0.0133606677
## 49:       6   ORF40 0.4259739 0.9237294 0.2132357 0.059173405 0.0133606677
## 50:       6   ORF42 0.4259739 0.9237294 0.2132357 0.059173405 0.0133606677
## 51:       6   ORF43 0.4259739 0.9237294 0.2132357 0.059173405 0.0133606677
## 52:       6   ORF44 0.4259739 0.9237294 0.2132357 0.059173405 0.0133606677
## 53:       6   ORF46 0.4259739 0.9237294 0.2132357 0.059173405 0.0133606677
## 54:       6   ORF48 0.4259739 0.9237294 0.2132357 0.059173405 0.0133606677
## 55:       6   ORF58 0.4259739 0.9237294 0.2132357 0.059173405 0.0133606677
## 56:       6   ORF59 0.4259739 0.9237294 0.2132357 0.059173405 0.0133606677
## 57:       6   ORF62 0.4259739 0.9237294 0.2132357 0.059173405 0.0133606677
## 58:       6   ORF68 0.4259739 0.9237294 0.2132357 0.059173405 0.0133606677
## 59:       7   ORF12 0.7534348 0.9633886 0.3842029 0.029206391 0.0065440020
## 60:       7   ORF13 0.7534348 0.9633886 0.3842029 0.029206391 0.0065440020
## 61:       7   ORF15 0.7534348 0.9633886 0.3842029 0.029206391 0.0065440020
## 62:       7   ORF16 0.7534348 0.9633886 0.3842029 0.029206391 0.0065440020
## 63:       7   ORF35 0.7534348 0.9633886 0.3842029 0.029206391 0.0065440020
## 64:       7   ORF41 0.7534348 0.9633886 0.3842029 0.029206391 0.0065440020
## 65:       7   ORF52 0.7534348 0.9633886 0.3842029 0.029206391 0.0065440020
## 66:       7   ORF54 0.7534348 0.9633886 0.3842029 0.029206391 0.0065440020
## 67:       7   ORF57 0.7534348 0.9633886 0.3842029 0.029206391 0.0065440020
## 68:       7   ORF60 0.7534348 0.9633886 0.3842029 0.029206391 0.0065440020
## 69:       7   ORF71 0.7534348 0.9633886 0.3842029 0.029206391 0.0065440020
## 70:       7   ORF72 0.7534348 0.9633886 0.3842029 0.029206391 0.0065440020
## 71:       8   ORF28 0.6952835 0.9537163 0.3539399 0.034395509 0.0080458063
## 72:       9   ORF32 0.8227913 0.9727877 0.4525900 0.022285232 0.0049976989
## 73:      10   ORF37 0.7397556 0.9733276 0.2732995 0.034743538 0.0055867404
## 74:      10   ORF51 0.7397556 0.9733276 0.2732995 0.034743538 0.0055867404
## 75:      10   ORF55 0.7397556 0.9733276 0.2732995 0.034743538 0.0055867404
## 76:      10   ORF76 0.7397556 0.9733276 0.2732995 0.034743538 0.0055867404
## 77:      11   ORF45 0.8804243 0.9766816 0.6065812 0.015856293 0.0042790537
## 78:      12 ORF64_1 0.6305561 0.9654082 0.2060473 0.047671283 0.0073158517
## 79:      12   ORF75 0.6305561 0.9654082 0.2060473 0.047671283 0.0073158517
##     cluster    gene        si        au        bp       se.si        se.au
##           se.bp          v         c      pchi
##           <num>      <num>     <num>     <num>
##  1: 0.004382320 -1.9080042 1.0047125 0.7086633
##  2: 0.004382320 -1.9080042 1.0047125 0.7086633
##  3: 0.004382320 -1.9080042 1.0047125 0.7086633
##  4: 0.004382320 -1.9080042 1.0047125 0.7086633
##  5: 0.004382320 -1.9080042 1.0047125 0.7086633
##  6: 0.004382320 -1.9080042 1.0047125 0.7086633
##  7: 0.004382320 -1.9080042 1.0047125 0.7086633
##  8: 0.004382320 -1.9080042 1.0047125 0.7086633
##  9: 0.004382320 -1.9080042 1.0047125 0.7086633
## 10: 0.004382320 -1.9080042 1.0047125 0.7086633
## 11: 0.004382320 -1.9080042 1.0047125 0.7086633
## 12: 0.005151593 -0.9742975 0.6289552 0.1611733
## 13: 0.005151593 -0.9742975 0.6289552 0.1611733
## 14: 0.005151593 -0.9742975 0.6289552 0.1611733
## 15: 0.005151593 -0.9742975 0.6289552 0.1611733
## 16: 0.005151593 -0.9742975 0.6289552 0.1611733
## 17: 0.005151593 -0.9742975 0.6289552 0.1611733
## 18: 0.005151593 -0.9742975 0.6289552 0.1611733
## 19: 0.005151593 -0.9742975 0.6289552 0.1611733
## 20: 0.005151593 -0.9742975 0.6289552 0.1611733
## 21: 0.005151593 -0.9742975 0.6289552 0.1611733
## 22: 0.005151593 -0.9742975 0.6289552 0.1611733
## 23: 0.005151593 -0.9742975 0.6289552 0.1611733
## 24: 0.004380733 -2.0226622 1.1181723 0.2380321
## 25: 0.004380733 -2.0226622 1.1181723 0.2380321
## 26: 0.004380733 -2.0226622 1.1181723 0.2380321
## 27: 0.004380733 -2.0226622 1.1181723 0.2380321
## 28: 0.004380733 -2.0226622 1.1181723 0.2380321
## 29: 0.004380733 -2.0226622 1.1181723 0.2380321
## 30: 0.004380733 -2.0226622 1.1181723 0.2380321
## 31: 0.004380733 -2.0226622 1.1181723 0.2380321
## 32: 0.004380733 -2.0226622 1.1181723 0.2380321
## 33: 0.005264210 -1.1975818 0.9334403 0.7481233
## 34: 0.005264210 -1.1975818 0.9334403 0.7481233
## 35: 0.005246549 -0.8583044 1.0460582 0.8520751
## 36: 0.005246549 -0.8583044 1.0460582 0.8520751
## 37: 0.005246549 -0.8583044 1.0460582 0.8520751
## 38: 0.004298087 -0.3176844 1.1129287 0.5410819
## 39: 0.004298087 -0.3176844 1.1129287 0.5410819
## 40: 0.004298087 -0.3176844 1.1129287 0.5410819
## 41: 0.004298087 -0.3176844 1.1129287 0.5410819
## 42: 0.004298087 -0.3176844 1.1129287 0.5410819
## 43: 0.004298087 -0.3176844 1.1129287 0.5410819
## 44: 0.004298087 -0.3176844 1.1129287 0.5410819
## 45: 0.004298087 -0.3176844 1.1129287 0.5410819
## 46: 0.004298087 -0.3176844 1.1129287 0.5410819
## 47: 0.004298087 -0.3176844 1.1129287 0.5410819
## 48: 0.004298087 -0.3176844 1.1129287 0.5410819
## 49: 0.004298087 -0.3176844 1.1129287 0.5410819
## 50: 0.004298087 -0.3176844 1.1129287 0.5410819
## 51: 0.004298087 -0.3176844 1.1129287 0.5410819
## 52: 0.004298087 -0.3176844 1.1129287 0.5410819
## 53: 0.004298087 -0.3176844 1.1129287 0.5410819
## 54: 0.004298087 -0.3176844 1.1129287 0.5410819
## 55: 0.004298087 -0.3176844 1.1129287 0.5410819
## 56: 0.004298087 -0.3176844 1.1129287 0.5410819
## 57: 0.004298087 -0.3176844 1.1129287 0.5410819
## 58: 0.004298087 -0.3176844 1.1129287 0.5410819
## 59: 0.005146050 -0.7484892 1.0429501 0.8028759
## 60: 0.005146050 -0.7484892 1.0429501 0.8028759
## 61: 0.005146050 -0.7484892 1.0429501 0.8028759
## 62: 0.005146050 -0.7484892 1.0429501 0.8028759
## 63: 0.005146050 -0.7484892 1.0429501 0.8028759
## 64: 0.005146050 -0.7484892 1.0429501 0.8028759
## 65: 0.005146050 -0.7484892 1.0429501 0.8028759
## 66: 0.005146050 -0.7484892 1.0429501 0.8028759
## 67: 0.005146050 -0.7484892 1.0429501 0.8028759
## 68: 0.005146050 -0.7484892 1.0429501 0.8028759
## 69: 0.005146050 -0.7484892 1.0429501 0.8028759
## 70: 0.005146050 -0.7484892 1.0429501 0.8028759
## 71: 0.005047109 -0.6536509 1.0283561 0.0472282
## 72: 0.005288818 -0.9021608 1.0212811 0.7119572
## 73: 0.004694626 -0.6646276 1.2674918 0.5687337
## 74: 0.004694626 -0.6646276 1.2674918 0.5687337
## 75: 0.004694626 -0.6646276 1.2674918 0.5687337
## 76: 0.004694626 -0.6646276 1.2674918 0.5687337
## 77: 0.005255137 -1.1300012 0.8595819 0.6401450
## 78: 0.004253597 -0.4985031 1.3187164 0.5350996
## 79: 0.004253597 -0.4985031 1.3187164 0.5350996
##           se.bp          v         c      pchi

## [1] "NOIR_2" "ORF1"   "ORF36"  "ORF59"  "ORF8"   "ORF39"  "ORF62"  "ORF48"
## [1] 8
##  [1] "ORF2"    "ORF3"    "ORF11"   "ORF14"   "ORF18"   "ORF19"   "ORF26"  
##  [8] "ORF29"   "ORF49"   "ORF66_1" "ORF73"   "ORF74"   "ORF8"    "ORF22"  
## [15] "ORF23"   "ORF24"   "ORF25"   "ORF27"   "ORF33"   "ORF35.5" "ORF36"  
## [22] "ORF39"   "CTO"     "ORF40"   "ORF42"   "ORF43"   "ORF44"   "ORF46"  
## [29] "ORF48"   "ORF58"   "ORF59"   "ORF62"   "ORF68"
## [1] 33

Selected number of clusters: 12

## Key: <cluster>
##     cluster    gene        si        au        bp       se.si        se.au
##       <int>  <char>     <num>     <num>     <num>       <num>        <num>
##  1:       1    ORF1 0.9886267 0.9982085 0.8168145 0.002477789 0.0004963390
##  2:       1    ORF5 0.9886267 0.9982085 0.8168145 0.002477789 0.0004963390
##  3:       1   ORF10 0.9886267 0.9982085 0.8168145 0.002477789 0.0004963390
##  4:       1   ORF17 0.9886267 0.9982085 0.8168145 0.002477789 0.0004963390
##  5:       1   ORF30 0.9886267 0.9982085 0.8168145 0.002477789 0.0004963390
##  6:       1   ORF53 0.9886267 0.9982085 0.8168145 0.002477789 0.0004963390
##  7:       1   ORF63 0.9886267 0.9982085 0.8168145 0.002477789 0.0004963390
##  8:       1 ORF65_1 0.9886267 0.9982085 0.8168145 0.002477789 0.0004963390
##  9:       1 ORF67_1 0.9886267 0.9982085 0.8168145 0.002477789 0.0004963390
## 10:       1   ORF69 0.9886267 0.9982085 0.8168145 0.002477789 0.0004963390
## 11:       1  NOIR_2 0.9886267 0.9982085 0.8168145 0.002477789 0.0004963390
## 12:       2    ORF2 0.7943269 0.9455606 0.6350814 0.023059291 0.0085043753
## 13:       2    ORF3 0.7943269 0.9455606 0.6350814 0.023059291 0.0085043753
## 14:       2   ORF11 0.7943269 0.9455606 0.6350814 0.023059291 0.0085043753
## 15:       2   ORF14 0.7943269 0.9455606 0.6350814 0.023059291 0.0085043753
## 16:       2   ORF18 0.7943269 0.9455606 0.6350814 0.023059291 0.0085043753
## 17:       2   ORF19 0.7943269 0.9455606 0.6350814 0.023059291 0.0085043753
## 18:       2   ORF26 0.7943269 0.9455606 0.6350814 0.023059291 0.0085043753
## 19:       2   ORF29 0.7943269 0.9455606 0.6350814 0.023059291 0.0085043753
## 20:       2   ORF49 0.7943269 0.9455606 0.6350814 0.023059291 0.0085043753
## 21:       2 ORF66_1 0.7943269 0.9455606 0.6350814 0.023059291 0.0085043753
## 22:       2   ORF73 0.7943269 0.9455606 0.6350814 0.023059291 0.0085043753
## 23:       2   ORF74 0.7943269 0.9455606 0.6350814 0.023059291 0.0085043753
## 24:       3    ORF4 0.9936064 0.9991577 0.8171322 0.001491305 0.0002494995
## 25:       3    ORF9 0.9936064 0.9991577 0.8171322 0.001491305 0.0002494995
## 26:       3   ORF20 0.9936064 0.9991577 0.8171322 0.001491305 0.0002494995
## 27:       3   ORF21 0.9936064 0.9991577 0.8171322 0.001491305 0.0002494995
## 28:       3   ORF31 0.9936064 0.9991577 0.8171322 0.001491305 0.0002494995
## 29:       3   ORF34 0.9936064 0.9991577 0.8171322 0.001491305 0.0002494995
## 30:       3   ORF38 0.9936064 0.9991577 0.8171322 0.001491305 0.0002494995
## 31:       3   ORF50 0.9936064 0.9991577 0.8171322 0.001491305 0.0002494995
## 32:       3   ORF61 0.9936064 0.9991577 0.8171322 0.001491305 0.0002494995
## 33:       4    ORF6 0.9056246 0.9834563 0.6041646 0.013300135 0.0032140854
## 34:       4   ORF70 0.9056246 0.9834563 0.6041646 0.013300135 0.0032140854
## 35:       5    ORF7 0.8075925 0.9715685 0.4255348 0.023970405 0.0052270304
## 36:       5   ORF56 0.8075925 0.9715685 0.4255348 0.023970405 0.0052270304
## 37:       5  NOIR_1 0.8075925 0.9715685 0.4255348 0.023970405 0.0052270304
## 38:       6    ORF8 0.4259739 0.9237294 0.2132357 0.059173405 0.0133606677
## 39:       6   ORF22 0.4259739 0.9237294 0.2132357 0.059173405 0.0133606677
## 40:       6   ORF23 0.4259739 0.9237294 0.2132357 0.059173405 0.0133606677
## 41:       6   ORF24 0.4259739 0.9237294 0.2132357 0.059173405 0.0133606677
## 42:       6   ORF25 0.4259739 0.9237294 0.2132357 0.059173405 0.0133606677
## 43:       6   ORF27 0.4259739 0.9237294 0.2132357 0.059173405 0.0133606677
## 44:       6   ORF33 0.4259739 0.9237294 0.2132357 0.059173405 0.0133606677
## 45:       6 ORF35.5 0.4259739 0.9237294 0.2132357 0.059173405 0.0133606677
## 46:       6   ORF36 0.4259739 0.9237294 0.2132357 0.059173405 0.0133606677
## 47:       6   ORF39 0.4259739 0.9237294 0.2132357 0.059173405 0.0133606677
## 48:       6     CTO 0.4259739 0.9237294 0.2132357 0.059173405 0.0133606677
## 49:       6   ORF40 0.4259739 0.9237294 0.2132357 0.059173405 0.0133606677
## 50:       6   ORF42 0.4259739 0.9237294 0.2132357 0.059173405 0.0133606677
## 51:       6   ORF43 0.4259739 0.9237294 0.2132357 0.059173405 0.0133606677
## 52:       6   ORF44 0.4259739 0.9237294 0.2132357 0.059173405 0.0133606677
## 53:       6   ORF46 0.4259739 0.9237294 0.2132357 0.059173405 0.0133606677
## 54:       6   ORF48 0.4259739 0.9237294 0.2132357 0.059173405 0.0133606677
## 55:       6   ORF58 0.4259739 0.9237294 0.2132357 0.059173405 0.0133606677
## 56:       6   ORF59 0.4259739 0.9237294 0.2132357 0.059173405 0.0133606677
## 57:       6   ORF62 0.4259739 0.9237294 0.2132357 0.059173405 0.0133606677
## 58:       6   ORF68 0.4259739 0.9237294 0.2132357 0.059173405 0.0133606677
## 59:       7   ORF12 0.7534348 0.9633886 0.3842029 0.029206391 0.0065440020
## 60:       7   ORF13 0.7534348 0.9633886 0.3842029 0.029206391 0.0065440020
## 61:       7   ORF15 0.7534348 0.9633886 0.3842029 0.029206391 0.0065440020
## 62:       7   ORF16 0.7534348 0.9633886 0.3842029 0.029206391 0.0065440020
## 63:       7   ORF35 0.7534348 0.9633886 0.3842029 0.029206391 0.0065440020
## 64:       7   ORF41 0.7534348 0.9633886 0.3842029 0.029206391 0.0065440020
## 65:       7   ORF52 0.7534348 0.9633886 0.3842029 0.029206391 0.0065440020
## 66:       7   ORF54 0.7534348 0.9633886 0.3842029 0.029206391 0.0065440020
## 67:       7   ORF57 0.7534348 0.9633886 0.3842029 0.029206391 0.0065440020
## 68:       7   ORF60 0.7534348 0.9633886 0.3842029 0.029206391 0.0065440020
## 69:       7   ORF71 0.7534348 0.9633886 0.3842029 0.029206391 0.0065440020
## 70:       7   ORF72 0.7534348 0.9633886 0.3842029 0.029206391 0.0065440020
## 71:       8   ORF28 0.6952835 0.9537163 0.3539399 0.034395509 0.0080458063
## 72:       9   ORF32 0.8227913 0.9727877 0.4525900 0.022285232 0.0049976989
## 73:      10   ORF37 0.7397556 0.9733276 0.2732995 0.034743538 0.0055867404
## 74:      10   ORF51 0.7397556 0.9733276 0.2732995 0.034743538 0.0055867404
## 75:      10   ORF55 0.7397556 0.9733276 0.2732995 0.034743538 0.0055867404
## 76:      10   ORF76 0.7397556 0.9733276 0.2732995 0.034743538 0.0055867404
## 77:      11   ORF45 0.8804243 0.9766816 0.6065812 0.015856293 0.0042790537
## 78:      12 ORF64_1 0.6305561 0.9654082 0.2060473 0.047671283 0.0073158517
## 79:      12   ORF75 0.6305561 0.9654082 0.2060473 0.047671283 0.0073158517
##     cluster    gene        si        au        bp       se.si        se.au
##           se.bp          v         c      pchi
##           <num>      <num>     <num>     <num>
##  1: 0.004382320 -1.9080042 1.0047125 0.7086633
##  2: 0.004382320 -1.9080042 1.0047125 0.7086633
##  3: 0.004382320 -1.9080042 1.0047125 0.7086633
##  4: 0.004382320 -1.9080042 1.0047125 0.7086633
##  5: 0.004382320 -1.9080042 1.0047125 0.7086633
##  6: 0.004382320 -1.9080042 1.0047125 0.7086633
##  7: 0.004382320 -1.9080042 1.0047125 0.7086633
##  8: 0.004382320 -1.9080042 1.0047125 0.7086633
##  9: 0.004382320 -1.9080042 1.0047125 0.7086633
## 10: 0.004382320 -1.9080042 1.0047125 0.7086633
## 11: 0.004382320 -1.9080042 1.0047125 0.7086633
## 12: 0.005151593 -0.9742975 0.6289552 0.1611733
## 13: 0.005151593 -0.9742975 0.6289552 0.1611733
## 14: 0.005151593 -0.9742975 0.6289552 0.1611733
## 15: 0.005151593 -0.9742975 0.6289552 0.1611733
## 16: 0.005151593 -0.9742975 0.6289552 0.1611733
## 17: 0.005151593 -0.9742975 0.6289552 0.1611733
## 18: 0.005151593 -0.9742975 0.6289552 0.1611733
## 19: 0.005151593 -0.9742975 0.6289552 0.1611733
## 20: 0.005151593 -0.9742975 0.6289552 0.1611733
## 21: 0.005151593 -0.9742975 0.6289552 0.1611733
## 22: 0.005151593 -0.9742975 0.6289552 0.1611733
## 23: 0.005151593 -0.9742975 0.6289552 0.1611733
## 24: 0.004380733 -2.0226622 1.1181723 0.2380321
## 25: 0.004380733 -2.0226622 1.1181723 0.2380321
## 26: 0.004380733 -2.0226622 1.1181723 0.2380321
## 27: 0.004380733 -2.0226622 1.1181723 0.2380321
## 28: 0.004380733 -2.0226622 1.1181723 0.2380321
## 29: 0.004380733 -2.0226622 1.1181723 0.2380321
## 30: 0.004380733 -2.0226622 1.1181723 0.2380321
## 31: 0.004380733 -2.0226622 1.1181723 0.2380321
## 32: 0.004380733 -2.0226622 1.1181723 0.2380321
## 33: 0.005264210 -1.1975818 0.9334403 0.7481233
## 34: 0.005264210 -1.1975818 0.9334403 0.7481233
## 35: 0.005246549 -0.8583044 1.0460582 0.8520751
## 36: 0.005246549 -0.8583044 1.0460582 0.8520751
## 37: 0.005246549 -0.8583044 1.0460582 0.8520751
## 38: 0.004298087 -0.3176844 1.1129287 0.5410819
## 39: 0.004298087 -0.3176844 1.1129287 0.5410819
## 40: 0.004298087 -0.3176844 1.1129287 0.5410819
## 41: 0.004298087 -0.3176844 1.1129287 0.5410819
## 42: 0.004298087 -0.3176844 1.1129287 0.5410819
## 43: 0.004298087 -0.3176844 1.1129287 0.5410819
## 44: 0.004298087 -0.3176844 1.1129287 0.5410819
## 45: 0.004298087 -0.3176844 1.1129287 0.5410819
## 46: 0.004298087 -0.3176844 1.1129287 0.5410819
## 47: 0.004298087 -0.3176844 1.1129287 0.5410819
## 48: 0.004298087 -0.3176844 1.1129287 0.5410819
## 49: 0.004298087 -0.3176844 1.1129287 0.5410819
## 50: 0.004298087 -0.3176844 1.1129287 0.5410819
## 51: 0.004298087 -0.3176844 1.1129287 0.5410819
## 52: 0.004298087 -0.3176844 1.1129287 0.5410819
## 53: 0.004298087 -0.3176844 1.1129287 0.5410819
## 54: 0.004298087 -0.3176844 1.1129287 0.5410819
## 55: 0.004298087 -0.3176844 1.1129287 0.5410819
## 56: 0.004298087 -0.3176844 1.1129287 0.5410819
## 57: 0.004298087 -0.3176844 1.1129287 0.5410819
## 58: 0.004298087 -0.3176844 1.1129287 0.5410819
## 59: 0.005146050 -0.7484892 1.0429501 0.8028759
## 60: 0.005146050 -0.7484892 1.0429501 0.8028759
## 61: 0.005146050 -0.7484892 1.0429501 0.8028759
## 62: 0.005146050 -0.7484892 1.0429501 0.8028759
## 63: 0.005146050 -0.7484892 1.0429501 0.8028759
## 64: 0.005146050 -0.7484892 1.0429501 0.8028759
## 65: 0.005146050 -0.7484892 1.0429501 0.8028759
## 66: 0.005146050 -0.7484892 1.0429501 0.8028759
## 67: 0.005146050 -0.7484892 1.0429501 0.8028759
## 68: 0.005146050 -0.7484892 1.0429501 0.8028759
## 69: 0.005146050 -0.7484892 1.0429501 0.8028759
## 70: 0.005146050 -0.7484892 1.0429501 0.8028759
## 71: 0.005047109 -0.6536509 1.0283561 0.0472282
## 72: 0.005288818 -0.9021608 1.0212811 0.7119572
## 73: 0.004694626 -0.6646276 1.2674918 0.5687337
## 74: 0.004694626 -0.6646276 1.2674918 0.5687337
## 75: 0.004694626 -0.6646276 1.2674918 0.5687337
## 76: 0.004694626 -0.6646276 1.2674918 0.5687337
## 77: 0.005255137 -1.1300012 0.8595819 0.6401450
## 78: 0.004253597 -0.4985031 1.3187164 0.5350996
## 79: 0.004253597 -0.4985031 1.3187164 0.5350996
##           se.bp          v         c      pchi

## [1] "NOIR_2" "ORF1"   "ORF36"  "ORF59"  "ORF8"   "ORF39"  "ORF62"  "ORF48"
## [1] 8
##  [1] "ORF2"    "ORF3"    "ORF11"   "ORF14"   "ORF18"   "ORF19"   "ORF26"  
##  [8] "ORF29"   "ORF49"   "ORF66_1" "ORF73"   "ORF74"   "ORF8"    "ORF22"  
## [15] "ORF23"   "ORF24"   "ORF25"   "ORF27"   "ORF33"   "ORF35.5" "ORF36"  
## [22] "ORF39"   "CTO"     "ORF40"   "ORF42"   "ORF43"   "ORF44"   "ORF46"  
## [29] "ORF48"   "ORF58"   "ORF59"   "ORF62"   "ORF68"
## [1] 33

Remove genes from clusters ?

##  [1] "ORF2"    "ORF3"    "ORF11"   "ORF14"   "ORF18"   "ORF19"   "ORF26"  
##  [8] "ORF29"   "ORF49"   "ORF66_1" "ORF73"   "ORF74"   "ORF8"    "ORF22"  
## [15] "ORF23"   "ORF24"   "ORF25"   "ORF27"   "ORF33"   "ORF35.5" "ORF36"  
## [22] "ORF39"   "CTO"     "ORF40"   "ORF42"   "ORF43"   "ORF44"   "ORF46"  
## [29] "ORF48"   "ORF58"   "ORF59"   "ORF62"   "ORF68"
## [1] 33
## No genes were removed from their corresponding clusters.
##     cluster     N
##       <int> <int>
##  1:       6    21
##  2:       2    12
##  3:       7    12
##  4:       1    11
##  5:       3     9
##  6:      10     4
##  7:       5     3
##  8:       4     2
##  9:      12     2
## 10:       8     1
## 11:       9     1
## 12:      11     1

Merge cluster stats

Assigning genes to clusters

Summarize and melt

Heatmaps

Normalized Expression

Expression delta ~ 6 hpi

Z-score of expression delta ~ 6 hpi

ORF kinetics, according to literature-based kinetic classes

Barplot of mean and SD

Figure 4 REVIEW - Mean and SD with linear connection

Mean and SD with loess function

Mean and SD with linear connection - Figure 4

Each replicate with loess

ORF kinetics, according to de-novo kinetic classes

Mean and SD with linear connection

Figure 5 REVIEW - Mean and SD with linear connection

Compare literature and de novo kinetic classes

NA shows the number of genes where the clustering did not yield an unambiguous result.

Combined Kinetic classes

De Novo Clusters

Literature clusters